Related papers: L-infinity optimization to linear spaces and phylo…
Given natural limitations on the length DNA sequences, designing phylogenetic reconstruction methods which are reliable under limited information is a crucial endeavor. There have been two approaches to this problem: reconstructing partial…
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 a recent series of papers devoted to the…
We study network loss tomography based on observing average loss rates over a set of paths forming a tree -- a severely underdetermined linear problem for the unknown link loss probabilities. We examine in detail the role of sparsity as a…
Phylogenetic networks are generalizations of trees that allow for the modeling of non-tree like evolutionary processes. Split networks give a useful way to construct networks with intuitive distance structures induced from the associated…
Shortest paths in treespace, which represent minimal deformations between trees, are unique and can be computed in polynomial time. The ability to quickly compute shortest paths has enabled new approaches for statistical analysis of…
Phylogenetic (i.e. leaf-labeled) trees play a fundamental role in evolutionary research. A typical problem is to reconstruct such trees from data like DNA alignments (whose columns are often referred to as characters), and a simple…
Phylogenetic networks which are, as opposed to trees, suitable to describe processes like hybridization and horizontal gene transfer, play a substantial role in evolutionary research. However, while non-treelike events need to be taken into…
The problem of finding suitable point embedding or geometric configurations given only Euclidean distance information of point pairs arises both as a core task and as a sub-problem in a variety of machine learning applications. In this…
We study the question of reconstructing a weighted, directed network up to isomorphism from its motifs. In order to tackle this question we first relax the usual (strong) notion of graph isomorphism to obtain a relaxation that we call weak…
In this paper, we present a flexible and probabilistic framework for tracking topological features in time-varying scalar fields using merge trees and partial optimal transport. Merge trees are topological descriptors that record the…
Accurate estimation of evolutionary distances between taxa is important for many phylogenetic reconstruction methods. In the case of bacteria, distances can be estimated using a range of different evolutionary models, from single nucleotide…
A geophylogeny is a phylogenetic tree (or dendrogram) where each leaf (e.g. biological taxon) has an associated geographic location (site). To clearly visualize a geophylogeny, the tree is typically represented as a crossing-free drawing…
The problem of comparing trees representing the evolutionary histories of cancerous tumors has turned out to be crucial, since there is a variety of different methods which typically infer multiple possible trees. A departure from the…
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…
Motivated by applications to low-rank matrix completion, we give a combinatorial characterization of the independent sets in the algebraic matroid associated to the collection of $m\times n$ rank-2 matrices and $n\times n$ skew-symmetric…
We have developed an alignment-free method that calculates phylogenetic distances using a maximum likelihood approach for a model of sequence change on patterns that are discovered in unaligned sequences. To evaluate the phylogenetic…
With the aim of estimating the abundance map from observations only, linear unmixing approaches are not always suitable to spectral images, especially when the number of bands is too small or when the spectra of the observed data are too…
Assume that we embed the path $P_n$ as a subgraph of a $2$-dimensional grid, namely, $P_k \times P_l$. Given such an embedding, we consider the ordered set of subpaths $L_1, L_2, \ldots , L_m$ which are maximal straight segments in the…
We study the problem of how well a tree metric is able to preserve the sum of pairwise distances of an arbitrary metric. This problem is closely related to low-stretch metric embeddings and is interesting by its own flavor from the line of…
Phylogenetic networks are a flexible model of evolution that can represent reticulate evolution and handle complex data. Tree-based networks, which are phylogenetic networks that have a spanning tree with the same root and leaf-set as the…