Related papers: Investigating the complexity of the double distanc…
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…
The distance geometry problem asks to find a realization of a given simple edge-weighted graph in a Euclidean space of given dimension K, where the edges are realized as straight segments of lengths equal (or as close as possible) to the…
A "genome structure" is a labeled directed graph with vertices of degree 1 or 2. A set of operations over such graphs is fixed, and each of the operations has a certain cost, a strictly positive number. The transformation problem consists…
We are concerned with linear redundancy storage schemes regarding their ability to provide concurrent (local) recovery of multiple data objects. This paper initiates a study of such systems within the classical coding theory. We show how we…
Error-tolerant graph matching gathers an important family of problems. These problems aim at finding correspondences between two graphs while integrating an error model. In the Graph Edit Distance (GED) problem, the insertion/deletion of…
It is an open question whether there exists a polynomial-time algorithm for computing the rotation distances between pairs of extended ordered binary trees. The problem of computing the rotation distance between an arbitrary pair of trees,…
Phylogenetic networks are generalizations of trees that allow for the modeling of non-tree like evolutionary processes. Split networks give a useful way to construct networks with intuitive distance structures induced from the associated…
Ancestral sequence reconstruction is a key task in computational biology. It consists in inferring a molecular sequence at an ancestral species of a known phylogeny, given descendant sequences at the tip of the tree. In addition to its many…
Phylogenetic trees illustrate the evolutionary history of genes and species. In most cases, although genes evolve along with the species they belong to, a species tree and gene tree are not identical, because of evolutionary events at the…
Motivation: Genome rearrangement plays an important role in evolutionary biology and has profound impacts on phenotype in organisms ranging from microbes to humans. The mechanisms for genome rearrangement events remain unclear. Lots of…
Geometry and topology have generated impacts far beyond their pure mathematical primitive, providing a solid foundation for many applicable tools. Typically, real-world data are represented as vectors, forming a linear subspace for a given…
Recent work has proven the existence of extreme inbreeding in a European ancestry sample taken from the contemporary UK population \cite{nature_01}. This result brings our attention again to a math problem related to inbreeding family trees…
A geometric graph is a combinatorial graph, endowed with a geometry that is inherited from its embedding in a Euclidean space. Formulation of a meaningful measure of (dis-)similarity in both the combinatorial and geometric structures of two…
We investigate structural and algorithmic advantages of a directed version of the well-researched class of distance-hereditary graphs. Since the previously defined distance-hereditary digraphs do not permit a recursive structure, we define…
Two genes are xenologs in the sense of Fitch if they are separated by at least one horizontal gene transfer event. Horizonal gene transfer is asymmetric in the sense that the transferred copy is distinguished from the one that remains…
Generative models are invaluable in many fields of science because of their ability to capture high-dimensional and complicated distributions, such as photo-realistic images, protein structures, and connectomes. How do we evaluate the…
For a code $C$ in a space with maximal distance $n$, we say that $C$ has symmetric distances if its distance set $S(C)$ is symmetric with respect to $n / 2$. In this paper, we prove that if $C$ is a binary code with length $2n$, constant…
More than ever, today we are left with the abundance of molecular data outpaced by the advancements of the phylogenomic methods. Especially in the case of presence of many genes over a set of species under the phylogeny question, more…
The reconstruction problem for permutations on $n$ elements from their erroneous patterns which are distorted by transpositions is presented in this paper. It is shown that for any $n \geq 3$ an unknown permutation is uniquely…
Genomes evolve as modules. In prokaryotes (and some eukaryotes), genetic material can be transferred between species and integrated into the genome via homologous or illegitimate recombination. There is little reason to imagine that the…