Related papers: Tanglegrams: a reduction tool for mathematical phy…
Biological phenotypes are products of complex evolutionary processes in which selective forces influence multiple biological trait measurements in unknown ways. Phylogenetic factor analysis disentangles these relationships across the…
Tree-based phylogenetic networks, which may be roughly defined as leaf-labeled networks built by adding arcs only between the original tree edges, have elegant properties for modeling evolutionary histories. We answer an open question of…
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…
Phylogenetic networks are a generalization of evolutionary or phylogenetic trees that are commonly used to represent the evolution of species which cross with one another. A special type of phylogenetic network is an {\em $X$-cactus}, which…
Since Darwin, species trees have been used as a simplified description of the relationships which summarize the complicated network $N$ of reality. Recent evidence of hybridization and lateral gene transfer, however, suggest that there are…
Boundary labeling is a technique in computational geometry used to label sets of features in an illustration. It involves placing labels along an axis-parallel bounding box and connecting each label with its corresponding feature using…
Terms in the lambda-calculus can be represented as planar trees decorated with symbols for abstraction and application, and having variables as leaves. In this paper, we concentrate on the branches of such trees, rather than on the trees…
Phylogenetics is now fundamental in life sciences, providing insights into the earliest branches of life and the origins and spread of epidemics. However, finding suitable phylogenies from the vast space of possible trees remains…
Suppose N is a phylogenetic network indicating a complicated relationship among individuals and taxa. Often of interest is a much simpler network, for example, a species tree T, that summarizes the most fundamental relationships. The…
Phylogenetic networks are increasingly used in evolutionary biology to represent the history of species that have undergone reticulate events such as horizontal gene transfer, hybrid speciation and recombination. One of the most fundamental…
In this paper we present a fully lexicalized grammar formalism as a particularly attractive framework for the specification of natural language grammars. We discuss in detail Feature-based, Lexicalized Tree Adjoining Grammars (FB-LTAGs), a…
Probabilistic programming frameworks are powerful tools for statistical modelling and inference. They are not immediately generalisable to phylogenetic problems due to the particular computational properties of the phylogenetic tree object.…
This is a collection of articles, written as sections, on arithmetic properties of differential equations, holomorphic foliations, Gauss-Manin connections and Hodge loci. Each section is independent from the others and it has its own…
Phylogenetically informed k-mers, or phylo-k-mers for short, are k-mers that are predicted to appear within a given genomic region at predefined locations of a fixed phylogeny. Given a reference alignment for this genomic region and…
We would like to congratulate Lee, Nadler and Wasserman on their contribution to clustering and data reduction methods for high $p$ and low $n$ situations. A composite of clustering and traditional principal components analysis, treelets is…
The vast majority of real world classification problems are imbalanced, meaning there are far fewer data from the class of interest (the positive class) than from other classes. We propose two machine learning algorithms to handle highly…
A phylogenetic tree is a way to organize a finite set of species, individuals or other sources of related data. The species for which we have existing DNA data make up the set of leaves of the tree. The balanced minimal evolution method of…
Following Poupard's study of strictly ordered binary trees with respect to two parameters, namely, "end of minimal chain" and "parent of maximum leaf" a true Tree Calculus is being developed to solve a partial difference equation system and…
Rooted phylogenetic networks are rooted acyclic digraphs. They are used to model complex evolution where hybridization, recombination and other reticulation events play important roles. A rigorous definition of network compression is…
We study the problem of learning a latent tree graphical model where samples are available only from a subset of variables. We propose two consistent and computationally efficient algorithms for learning minimal latent trees, that is, trees…