Related papers: L-infinity optimization to linear spaces and phylo…
Distance-based approaches in phylogenetics such as Neighbor-Joining are a fast and popular approach for building trees. These methods take pairs of sequences from them construct a value that, in expectation, is additive under a stochastic…
We describe algorithms for finding the regression of t, a sequence of values, to the closest sequence s by mean squared error, so that s is always increasing (isotonicity) and so the values of two consecutive points do not increase by too…
Tree representations of (sets of) symmetric binary relations, or equivalently edge-colored undirected graphs, are of central interest, e.g.\ in phylogenomics. In this context symbolic ultrametrics play a crucial role. Symbolic ultrametrics…
We study the geometry of metrics and convexity structures on the space of phylogenetic trees, which is here realized as the tropical linear space of all \ ultrametrics. The ${\rm CAT}(0)$-metric of Billera-Holmes-Vogtman arises from the…
Semidirected networks have received interest in evolutionary biology as the appropriate generalization of unrooted trees to networks, in which some but not all edges are directed. Yet these networks lack proper theoretical study. We define…
The algebraic properties of flattenings and subflattenings provide direct methods for identifying edges in the true phylogeny -- and by extension the complete tree -- using pattern counts from a sequence alignment. The relatively small…
We address the problem of merging graph and feature-space information while learning a metric from structured data. Existing algorithms tackle the problem in an asymmetric way, by either extracting vectorized summaries of the graph…
The decomposition of a density function on a domain into a minimal sum of unimodal components is a fundamental problem in statistics, leading to the topological invariant of unimodal category of a density. This paper gives an efficient…
Trajectories represent the mobility of moving objects and thus is of great value in data mining applications. However, trajectory data is enormous in volume, so it is expensive to store and process the raw data directly. Trajectories are…
Phylogenetics begins with reconstructing biological family trees from genetic data. Since Nature is not limited to tree-like histories, we use networks to organize our data, and have discovered new polytopes, metric spaces, and simplicial…
Starting with a similarity function between objects, it is possible to define a distance metric on pairs of objects, and more generally on probability distributions over them. These distance metrics have a deep basis in functional analysis,…
The goal of this paper is to study the similarity between sequences using a distance between the \emph{context} trees associated to the sequences. These trees are defined in the framework of \emph{Sparse Probabilistic Suffix Trees} (SPST),…
This work presents novel algorithms for learning Bayesian network structures with bounded treewidth. Both exact and approximate methods are developed. The exact method combines mixed-integer linear programming formulations for structure…
In the longest plane spanning tree problem, we are given a finite planar point set $\mathcal{P}$, and our task is to find a plane (i.e., noncrossing) spanning tree for $\mathcal{P}$ with maximum total Euclidean edge length. Despite more…
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…
When estimating a phylogeny from a multiple sequence alignment, researchers often assume the absence of recombination. However, if recombination is present, then tree estimation and all downstream analyses will be impacted, because…
The contributions of the paper span theoretical and implementational results. First, we prove that Kd-trees can be extended to spaces in which the distance is measured with an arbitrary Bregman divergence. Perhaps surprisingly, this shows…
In this paper we show how to recover a spectral approximations to broad classes of structured matrices using only a polylogarithmic number of adaptive linear measurements to either the matrix or its inverse. Leveraging this result we obtain…
The goal of this work is to decompose random populations with a genealogy in subfamilies of a given degree of kinship and to obtain a notion of infinitely divisible genealogies. We model the genealogical structure of a population by…
We devise a generalization of tree approximation that generates conforming meshes, i.e., meshes with a particular structure like edge-to-edge triangulations. A key feature of this generalization is that the choices of the cells to be…