Related papers: On the complexity of computing MP distance between…
Phylogenetic tree reconstruction is traditionally based on multiple sequence alignments (MSAs) and heavily depends on the validity of this information bottleneck. With increasing sequence divergence, the quality of MSAs decays quickly.…
It has remained an open question for some time whether, given a set of not necessarily binary (i.e. "nonbinary") trees T on a set of taxa X, it is possible to determine in time f(r).poly(m) whether there exists a phylogenetic network that…
We compare the phylogenetic tensors for various trees and networks for two, three and four taxa. If the probability spaces between one tree or network and another are not identical then there will be phylogenetic tensors that could have…
This work proposes a tentative model for the calculation of dimensionless distances between phonemes; sounds are described with binary distinctive features and distances show linear consistency in terms of such features. The model can be…
The Hausdorff distance is a relatively new measure of similarity of graphs. The notion of the Hausdorff distance considers a special kind of a common subgraph of the compared graphs and depends on the structural properties outside of the…
To the known fact that Parsimony method sometimes fails on the problem of inferring species trees from gene trees, here we proved that no mater of what topology the true 9-taxon and greater species tree is the only thing one needs to break…
Motivated by alignment of correlated sparse random graphs, we introduce a hypothesis testing problem of deciding whether or not two random trees are correlated. We obtain sufficient conditions under which this testing is impossible or…
Applications in machine learning and data mining require computing pairwise Lp distances in a data matrix A. For massive high-dimensional data, computing all pairwise distances of A can be infeasible. In fact, even storing A or all pairwise…
Maximum distance separable (MDS) are constructed to required specifications. The codes are explicitly given over finite fields with efficient encoding and decoding algorithms. Series of such codes over finite fields with ratio of distance…
In phylogenetic studies, biologists often wish to estimate the ancestral discrete character state at an interior vertex $v$ of an evolutionary tree $T$ from the states that are observed at the leaves of the tree. A simple and fast…
We introduce a semiparametric approach to neighbor-based classification. We build off the recently proposed Boundary Trees algorithm by Mathy et al.(2015) which enables fast neighbor-based classification, regression and retrieval in large…
This paper introduces PhyloLM, a method adapting phylogenetic algorithms to Large Language Models (LLMs) to explore whether and how they relate to each other and to predict their performance characteristics. Our method calculates a…
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…
A new class of distances appropriate for measuring similarity relations between sequences, say one type of similarity per distance, is studied. We propose a new ``normalized information distance'', based on the noncomputable notion of…
This work addresses the problem of computing measures of recognisable sets of infinite trees. An algorithm is provided to compute the probability measure of a tree language recognisable by a weak alternating automaton, or equivalently…
The problem of comparing probability distributions is at the heart of many tasks in statistics and machine learning. Established comparison methods treat the standard setting that the distributions are supported in the same space. Recently,…
Rotation distance between rooted binary trees is the minimum number of simple rotations needed to transform one tree into the other. Computing the rotation distance between a pair of rooted trees can be quickly reduced in cases where there…
Phylogenetic trees represent certain species and their likely ancestors. In such a tree, present-day species are leaves and an edge from u to v indicates that u is an ancestor of v. Weights on these edges indicate the phylogenetic distance.…
Phylogenetic trees describe the relationships between species in the evolutionary process, and provide information about the rates of diversification. To understand the mechanisms behind macroevolution, we consider a class of multitype…
In this thesis, Minimal Partitioning (MP) algorithm, an innovative algorithm for enumerating all the spanning trees in an undirected graph is presented. While MP algorithm uses a computational tree graph to traverse all possible spanning…