Related papers: Phylogenetic tree constructing algorithms fit for …
The soft SVD is a robust matrix decomposition algorithm and a key component of matrix completion methods. However, computing the soft SVD for large sparse matrices is often impractical using conventional numerical methods for the SVD due to…
We introduce a simple algorithm for reconstructing phylogenies from multiple gene trees in the presence of incomplete lineage sorting, that is, when the topology of the gene trees may differ from that of the species tree. We show that our…
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…
In this work a composition-decomposition technique is presented that correlates tree eigenvectors with certain eigenvectors of an associated so-called skeleton forest. In particular, the matching properties of a skeleton determine the…
In this article, we construct a generalization of the Blum-Fran\c{c}ois Beta-splitting model for evolutionary trees, which was itself inspired by Aldous' Beta-splitting model on cladograms. The novelty of our approach allows for asymmetric…
Phylogenetic networks are a type of leaf-labelled, acyclic, directed graph used by biologists to represent the evolutionary history of species whose past includes reticulation events. A phylogenetic network is tree-child if each non-leaf…
In this paper, we address the well-known challenge in the numerical solution of time-fractional partial differential equations (TFPDEs), namely, that the dependence on all previous time levels leads to storage requirements that grow…
In this paper, we revisit the split decomposition of graphs and give new combinatorial and algorithmic results for the class of totally decomposable graphs, also known as the distance hereditary graphs, and for two non-trivial subclasses,…
Supertree construction is the process by which a set of phylogenetic trees, each on a subset of the overall set X of species, is combined into a tree on the full set S. The traditional use of supertree methods is the assembly of a large…
The supertree problem asking for a tree displaying a set of consistent input trees has been largely considered for the reconstruction of species trees. Here, we rather explore this framework for the sake of reconstructing a gene tree from a…
In this work, we answer an open problem in the study of phylogenetic networks. Phylogenetic trees are rooted binary trees in which all edges are directed away from the root, whereas phylogenetic networks are rooted acyclic digraphs. For the…
Construction of phylogenetic trees has traditionally focused on binary trees where all species appear on leaves, a problem for which numerous efficient solutions have been developed. Certain application domains though, such as viral…
Deciding whether there is a single tree -a supertree- that summarizes the evolutionary information in a collection of unrooted trees is a fundamental problem in phylogenetics. We consider two versions of this question: agreement and…
Sparse reduced-rank regression is an important tool to uncover meaningful dependence structure between large numbers of predictors and responses in many big data applications such as genome-wide association studies and social media…
A model of genomic sequence evolution on a species tree should include not only a sequence substitution process, but also a coalescent process, since different sites may evolve on different gene trees due to incomplete lineage sorting.…
Recently proposed budding tree is a decision tree algorithm in which every node is part internal node and part leaf. This allows representing every decision tree in a continuous parameter space, and therefore a budding tree can be jointly…
The tensor Singular Value Decomposition (t-SVD) for third order tensors that was proposed by Kilmer and Martin~\cite{2011kilmer} has been applied successfully in many fields, such as computed tomography, facial recognition, and video…
Eigendecomposition of symmetric matrices is at the heart of many computer vision algorithms. However, the derivatives of the eigenvectors tend to be numerically unstable, whether using the SVD to compute them analytically or using the Power…
In this paper, we present an exact algorithm for the Steiner tree problem. The algorithm is based on certain pre-computed index structures. Our algorithm offers a practical solution for the Steiner tree problems on graphs of large size and…
Evolutionary histories for species that cross with one another or exchange genetic material can be represented by leaf-labelled, directed graphs called phylogenetic networks. A major challenge in the burgeoning area of phylogenetic networks…