Related papers: A scale-free method for testing the proportionalit…
We introduce the tree distance, a new distance measure on graphs. The tree distance can be computed in polynomial time with standard methods from convex optimization. It is based on the notion of fractional isomorphism, a characterization…
We study the effectiveness of non-uniform randomized feature selection in decision tree classification. We experimentally evaluate two feature selection methodologies, based on information extracted from the provided dataset: $(i)$…
In this paper, we consider a tree inference problem motivated by the critical problem in single-cell genomics of reconstructing dynamic cellular processes from sequencing data. In particular, given a population of cells sampled from such a…
A metric phylogenetic tree relating a collection of taxa induces weighted rooted triples and weighted quartets for all subsets of three and four taxa, respectively. New intertaxon distances are defined that can be calculated from these…
In this article the results of Waddell and Azad (2009) are extended. In particular, the geometric percentage mean standard deviation measure of the fit of distances to a phylogenetic tree is adjusted for the number of parameters fitted to…
Often the factorization of differential cross sections results in the definition of fundamental hadronic functions/distributions which have a double-scale evolution, as provided by a pair of coupled equations. Typically, the two scales are…
We study the statistical properties of the sampled scale-free networks, deeply related to the proper identification of various real-world networks. We exploit three methods of sampling and investigate the topological properties such as…
A model of genomic sequence evolution on a species tree should include not only a sequence substitution process, but also a coalescent process, since different sites may evolve on different gene trees due to incomplete lineage sorting.…
Summary: Both theory and empirical evidence indicate that phylogenies (trees) of different genes (loci) do not display precisely matched topologies. This phylogenetic incongruence is attributed to the reticulated evolutionary history of…
Evolutionary events such as incomplete lineage sorting and lateral gene transfer constitute major problems for inferring species trees from gene trees, as they can sometimes lead to gene trees which conflict with the underlying species…
We investigate parameterized algorithms for computing the average-tree phylogenetic diversity (APD) in rooted phylogenetic networks, studying the problem under different structural parameters that capture the deviation of a network from a…
We investigated testing the likelihood of a phylogenetic tree by comparison to its subtree pruning and regrafting (SPR) neighbors, with or without re-optimizing branch lengths. This is inspired by aspects of Bayesian significance tests, and…
When we apply comparative phylogenetic analyses to genome data, it is a well-known problem and challenge that some of given species (or taxa) often have missing genes. In such a case, we have to impute a missing part of a gene tree from a…
This paper presents a spectral framework for quantifying the differentiation between graph data samples by introducing a novel metric named Graph Geodesic Distance (GGD). For two different graphs with the same number of nodes, our framework…
We present sublinear-time (randomized) algorithms for finding simple cycles of length at least $k\geq 3$ and tree-minors in bounded-degree graphs. The complexity of these algorithms is related to the distance of the graph from being…
Deciding whether a political districting plan was distorted by a hidden agenda, or whether it dilutes the voting power of some group, requires a neutral baseline for comparison. Remarkably, all nine U.S. Supreme Court justices have now…
The minimum linear arrangement problem on a network consists of finding the minimum sum of edge lengths that can be achieved when the vertices are arranged linearly. Although there are algorithms to solve this problem on trees in polynomial…
Distance-based regression model, as a nonparametric multivariate method, has been widely used to detect the association between variations in a distance or dissimilarity matrix for outcomes and predictor variables of interest in genetic…
Graphs are interesting structures: extremely useful to depict real-life problems, extremely easy to understand given a sketch, extremely complicated to represent formally, extremely complicated to compare. Phylogeny is the study of the…
In this paper, we present a simple model of scale-free networks that incorporates both preferential & random attachment and anti-preferential & random deletion at each time step. We derive the degree distribution analytically and show that…