Related papers: Laplacian Matrices for Extremely Balanced and Unba…
We study degenerate fully nonlinear free transmission problems, where the degeneracy rate varies in the domain. We prove optimal pointwise regularity depending on the degeneracy rate. Our arguments consist of perturbation methods, relating…
Phylogenetic networks represent evolutionary history of species and can record natural reticulate evolutionary processes such as horizontal gene transfer and gene recombination. This makes phylogenetic networks a more comprehensive…
Fossil-based palaeoclimate reconstruction is an important area of ecological science that has gained momentum in the backdrop of the global climate change debate. The hierarchical Bayesian paradigm provides an interesting platform for…
A recurring theme in the least squares approach to phylogenetics has been the discovery of elegant combinatorial formulas for the least squares estimates of edge lengths. These formulas have proved useful for the development of efficient…
Phylogenomics is a new field which applies to tools in phylogenetics to genome data. Due to a new technology and increasing amount of data, we face new challenges to analyze them over a space of phylogenetic trees. Because a space of…
Estimating phylogenetic trees, which depict the relationships between different species, from aligned sequence data (such as DNA, RNA, or proteins) is one of the main aims of evolutionary biology. However, tree reconstruction criteria like…
The so-called binary perfect phylogeny with persistent characters has recently been thoroughly studied in computational biology as it is less restrictive than the well known binary perfect phylogeny. Here, we focus on the notion of (binary)…
We introduce a new phylogenetic reconstruction algorithm which, unlike most previous rigorous inference techniques, does not rely on assumptions regarding the branch lengths or the depth of the tree. The algorithm returns a forest which is…
Phylogenetic trees describe the relationships between species in the evolutionary process, and provide information about the rates of diversification. To understand the mechanisms behind macroevolution, we consider a class of multitype…
Understanding the evolution of a set of genes or species is a fundamental problem in evolutionary biology. The problem we study here takes as input a set of trees describing {possibly discordant} evolutionary scenarios for a given set of…
In this paper, we study the multiplicity of the Laplacian eigenvalues of trees. It is known that for trees, integer Laplacian eigenvalues larger than $1$ are simple and also the multiplicity of Laplacian eigenvalue $1$ has been well studied…
This paper considers the problem of estimating high dimensional Laplacian constrained precision matrices by minimizing Stein's loss. We obtain a necessary and sufficient condition for existence of this estimator, that consists on checking…
We generalize the results from [X.-D. Zhang, X.-P. Lv, Y.-H. Chen, \textit{Ordering trees by the Laplacian coefficients}, Linear Algebra Appl. (2009), doi:10.1016/j.laa.2009.04.018] on the partial ordering of trees with given diameter. For…
Phylogenetic networks are a generalization of phylogenetic trees that allow for the representation of non-treelike evolutionary events, like recombination, hybridization, or lateral gene transfer. In this paper, we present and study a new…
Spanning trees are relevant to various aspects of networks. Generally, the number of spanning trees in a network can be obtained by computing a related determinant of the Laplacian matrix of the network. However, for a large generic…
Phylogenetic stochastic mapping is a method for reconstructing the history of trait changes on a phylogenetic tree relating species/organisms carrying the trait. State-of-the-art methods assume that the trait evolves according to a…
Identifying undocumented or potential future interactions among species is a challenge facing modern ecologists. Recent link prediction methods rely on trait data, however large species interaction databases are typically sparse and…
In phylogenetics, phylogenetic trees are rooted binary trees, whereas phylogenetic networks are rooted arbitrary acyclic digraphs. Edges are directed away from the root and leaves are uniquely labeled with taxa in phylogenetic networks. For…
In recent years, there has been an effort to extend the classical notion of phylogenetic balance, originally defined in the context of trees, to networks. One of the most natural ways to do this is with the so-called $B_2$ index. In this…
The stability of topological persistence is one of the fundamental issues in topological data analysis. Numerous methods have been proposed to address the stability of persistent modules or persistence diagrams. Recently, the concept of…