Related papers: Combinatorics of least squares trees
A new tree model is introduced based on ordered trees, by distinguishing exactly one child of each node that \emph{has} children. The basic enumeration leads to a cubic equation of the generating function. The extraction of its coefficients…
Jain's iterative rounding theorem is a well-known result in the area of approximation algorithms and, more broadly, in combinatorial optimization. The theorem asserts that LP relaxations of several problems in network design and…
We show the existence of regular combinatorial objects which previously were not known to exist. Specifically, for a wide range of the underlying parameters, we show the existence of non-trivial orthogonal arrays, t-designs, and t-wise…
The Rooted Maximum Leaf Outbranching problem consists in finding a spanning directed tree rooted at some prescribed vertex of a digraph with the maximum number of leaves. Its parameterized version asks if there exists such a tree with at…
Phylogenomics, even more so than traditional phylogenetics, needs to represent the uncertainty in evolutionary trees due to systematic error. Here we illustrate the analysis of genome-scale alignments of yeast, using robust measures of the…
An evolutionary tree (phylogenetic tree) is a binary, rooted, unordered tree that models the evolutionary history of currently living species in which leaves are labeled by species. In this paper, we investigate the problem of finding the…
The so-called constrained least mean-square algorithm is one of the most commonly used linear-equality-constrained adaptive filtering algorithms. Its main advantages are adaptability and relative simplicity. In order to gain analytical…
In Polyamorous Scheduling, we are given an edge-weighted graph and must find a periodic schedule of matchings in this graph which minimizes the maximal weighted waiting time between consecutive occurrences of the same edge. This NP-hard…
In the context of reconstructing phylogenetic networks from a collection of phylogenetic trees, several characterisations and subsequently algorithms have been established to reconstruct a phylogenetic network that collectively embeds all…
In combinatorial optimization, partial variable assignments are called persistent if they agree with some optimal solution. We propose persistency criteria for the multicut and max-cut problem as well as fast combinatorial routines to…
We consider the problem of ranking $N$ objects starting from a set of noisy pairwise comparisons provided by a crowd of equal workers. We assume that objects are endowed with intrinsic qualities and that the probability with which an object…
Phylogenetic networks are increasingly being considered as better suited to represent the complexity of the evolutionary relationships between species. One class of phylogenetic networks that has received a lot of attention recently is the…
We develop Clustered Random Forests, a random forests algorithm for clustered data, arising from independent groups that exhibit within-cluster dependence. The leaf-wise predictions for each decision tree making up clustered random forests…
Balanced minimum evolution (BME) is a statistically consistent distance-based method to reconstruct a phylogenetic tree from an alignment of molecular data. In 2000, Pauplin showed that the BME method is equivalent to optimizing a linear…
To find the least squares solution of a very large and inconsistent system of equations, one can employ the extended Kaczmarz algorithm. This method simultaneously removes the error term, such that a consistent system is asymptotically…
We study computational aspects of a key problem in robust statistics -- the penalized least trimmed squares (LTS) regression problem, a robust estimator that mitigates the influence of outliers in data by capping residuals with large…
Using the concept of Geometric Weakly Admissible Meshes together with an algorithm based on the classical QR factorization of matrices, we compute efficient points for discrete multivariate least squares approximation and Lagrange…
The phylogenetic tree space introduced by Billera, Holmes, and Vogtmann (BHV tree space) is a CAT(0) continuous space that represents trees with edge weights with an intrinsic geodesic distance measure. The geodesic distance measure unique…
Markov parameters play a key role in system identification. There exists many algorithms where these parameters are estimated using least-squares in a first, pre-processing, step, including subspace identification and multi-step…
We present the first fixed-parameter algorithm for constructing a tree-child phylogenetic network that displays an arbitrary number of binary input trees and has the minimum number of reticulations among all such networks. The algorithm…