Related papers: Combinatorics of least squares trees
The objective of clustering is to discover natural groups in datasets and to identify geometrical structures which might reside there, without assuming any prior knowledge on the characteristics of the data. The problem can be seen as…
It is a known fact that, given two rooted binary phylogenetic trees, the concept of maximum acyclic agreement forests is sufficient to compute hybridization networks with minimum hybridization number. In this work, we demonstrate by first…
As an alternative to parsimony analyses, stochastic models have been proposed (Lewis, 2001), (Nylander, et al., 2004) for morphological characters, so that maximum likelihood or Bayesian analyses may be used for phylogenetic inference. A…
In this paper, we review the problem of matrix completion and expose its intimate relations with algebraic geometry, combinatorics and graph theory. We present the first necessary and sufficient combinatorial conditions for matrices of…
Least squares trees, multi-dimensional scaling and Neighbor Nets are all different and popular ways of visualizing multi-dimensional data. The method of flexi-Weighted Least Squares (fWLS) is a powerful method of fitting phylogenetic trees,…
Latent variable models are an elegant framework for capturing rich probabilistic dependencies in many applications. However, current approaches typically parametrize these models using conditional probability tables, and learning relies…
Laguerre's rootfinding algorithm is highly recommended although most of its properties are known only by empirical evidence. In view of this, we prove the first sufficient convergence criterion. It is applicable to simple roots of…
We construct least squares formulations of PDEs with inhomogeneous essential boundary conditions, where boundary residuals are not measured in unpractical fractional Sobolev norms, but which formulations nevertheless are shown to yield a…
Many popular algorithms for searching the space of leaf-labelled trees are based on tree rearrangement operations. Under any such operation, the problem is reduced to searching a graph where vertices are trees and (undirected) edges are…
In linear combinatorial optimization, we aim to find $S^* = \arg\min_{S \in \mathcal{F}} \langle w,\mathbf{1}_S \rangle$ for a family $\mathcal{F} \subseteq 2^U$ over a ground set $U$ of $n$ elements. Traditionally, $w$ is known or…
Many real world networks exhibit edge heterogeneity with different pairs of nodes interacting with different intensities. Further, nodes with similar attributes tend to interact more with each other. Thus, in the presence of observed node…
We developed a least squares fitter used for extracting expected physics parameters from the correlated experimental data in high energy physics. This fitter considers the correlations among the observables and handles the nonlinearity…
Phylogenetic trees are leaf-labelled trees, where the leaves correspond to extant species (taxa), and the internal vertices represent ancestral species. The evolutionary history of a set of species can be explained by more than one…
It is required to find an optimal order of constructing the edges of a network so as to minimize the sum of the weighted connection times of relevant pairs of vertices. Construction can be performed anytime anywhere in the network, with a…
We investigate the tractability of a simple fusion of two fundamental structures on graphs, a spanning tree and a perfect matching. Specifically, we consider the following problem: given an edge-weighted graph, find a minimum-weight…
Given a directed graph $G$ on $n$ vertices with a special vertex $s$, the directed minimum degree spanning tree problem requires computing a incoming spanning tree rooted at $s$ whose maximum tree in-degree is the smallest among all such…
Distance-based methods such as UPGMA (Unweighted Pair Group Method with Arithmetic Mean) continue to play a significant role in phylogenetic research. We use polyhedral combinatorics to analyze the natural subdivision of the positive…
Recombining trinomial trees are a workhorse for modeling discrete-event systems in option pricing, logistics, and feedback control. Because each node stores a state-dependent quantity, a depth-$D$ tree naively yields $\mathcal{O}(3^{D})$…
We study the problem of sharing as many branching conditions of a given forest classifier or regressor as possible while keeping classification performance. As a constraint for preventing from accuracy degradation, we first consider the one…
The alternating least squares algorithm for CP and Tucker decomposition is dominated in cost by the tensor contractions necessary to set up the quadratic optimization subproblems. We introduce a novel family of algorithms that uses…