Related papers: Nested tree space: a geometric framework for co-ph…
We study two related probabilistic models of permutations and trees biased by their number of descents. Here, a descent in a permutation $\sigma$ is a pair of consecutive elements $\sigma(i), \sigma(i+1)$ such that $\sigma(i) >…
We exhibit an identity of abstract simplicial complexes between the well-studied complex of trees and the reduced minimal nested set complex of the partition lattice. We conclude that the order complex of the partition lattice can be…
In phylogenetics, evolution is traditionally represented in a tree-like manner. However, phylogenetic networks can be more appropriate for representing evolutionary events such as hybridization, horizontal gene transfer, and others. In…
Latent space models for network data characterize each node through a vector of latent features whose pairwise similarities define the edge probabilities among the pairs of nodes. Although this formulation has led to successful…
We study (unrooted) random forests on a graph where the probability of a forest is multiplicatively weighted by a parameter $\beta>0$ per edge. This is called the arboreal gas model, and the special case when $\beta=1$ is the uniform forest…
Ordered phases resulting from spontaneously broken continuous symmetries are effectively described by sigma models of maps to the coset space of Goldstone modes. A classic problem is to classify the topological sectors of the sigma model.…
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…
Causal fermion systems and Riemannian fermion systems are proposed as a framework for describing non-smooth geometries. In particular, this framework provides a setting for spinors on singular spaces. The underlying topological structures…
The doubled target space of the fundamental closed string is identified with its phase space and described by an almost para-Hermitian geometry. We explore this setup in the context of group manifolds which admit a maximally isotropic…
Suffix trees are a fundamental data structure in stringology, but their space usage, though linear, is an important problem for its applications. We design and implement a new compressed suffix tree targeted to highly repetitive texts, such…
We extend decision tree and random forest algorithms to product space manifolds: Cartesian products of Euclidean, hyperspherical, and hyperbolic manifolds. Such spaces have extremely expressive geometries capable of representing many…
This work addresses an enumeration problem on weighted bi-colored plane trees with prescribed vertex data, with all vertices labeled distinctly. We give a bijection proof of the enumeration formula originally due to Kochetkov, hence…
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…
We destroy a finite tree of size $n$ by cutting its edges one after the other and in uniform random order. Informally, the associated cut-tree describes the genealogy of the connected components created by this destruction process. We…
Many data are naturally modeled by an unobserved hierarchical structure. In this paper we propose a flexible nonparametric prior over unknown data hierarchies. The approach uses nested stick-breaking processes to allow for trees of…
In this paper we consider two aspects of the inverse problem of how to construct merge trees realizing a given barcode. Much of our investigation exploits a recently discovered connection between the symmetric group and barcodes in general…
Phylogenetic networks are a generalization of phylogenetic trees allowing for the representation of non-treelike evolutionary events such as hybridization. Typically, such networks have been analyzed based on their `level', i.e. based on…
Interactions and relations between objects may be pairwise or higher-order in nature, and so network-valued data are ubiquitous in the real world. The "space of networks", however, has a complex structure that cannot be adequately described…
The displayed tree phylogenetic network model is shown to sit as a natural submodel of the graphical model associated to a directed acyclic graph (DAG). This representation allows to derive a number of results about the displayed tree…
Inferential summaries of tree estimates are useful in the setting of evolutionary biology, where phylogenetic trees have been built from DNA data since the 1960's. In bioinformatics, psychometrics and data mining, hierarchical clustering…