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Finding the most parsimonious tree inside a phylogenetic network with respect to a given character is an NP-hard combinatorial optimization problem that for many network topologies is essentially inapproximable. In contrast, if the network…
Tree sets are abstract structures that can be used to model various tree-shaped objects in combinatorics. Finite tree sets can be represented by finite graph-theoretical trees. We extend this representation theory to infinite tree sets.…
Phylogenetic trees canonically arise as embeddings of phylogenetic networks. We recently showed that the problem of deciding if two phylogenetic networks embed the same sets of phylogenetic trees is computationally hard, \blue{in…
Most of major algorithms for phylogenetic tree reconstruction assume that sequences in the analyzed set either do not have any offspring, or that parent sequences can maximally mutate into just two descendants. The graph resulting from such…
A natural number N is said to be palindromic if its binary representation reads the same forwards and backwards. In this paper we study the quotients of two palindromic numbers and answer some basic questions about the resulting sets of…
Wavelet trees are widely used in the representation of sequences, permutations, text collections, binary relations, discrete points, and other succinct data structures. We show, however, that this still falls short of exploiting all of the…
The Horton-Strahler analysis is a graph-theoretic method to measure the bifurcation complexity of branching patterns, by defining a number called the order to each branch. The main result of this paper is a large deviation theorem for the…
Prime-based ordering which is proved to be admissible, is the encoding of indeterminates in power-products with prime numbers and ordering them by using the natural number order. Using Eiffel, four versions of Buchberger's improved…
In this paper we investigate undirected discrete graphical tree models when all the variables in the system are binary, where leaves represent the observable variables and where all the inner nodes are unobserved. A novel approach based on…
We discuss a notion of convergence for binary trees that is based on subtree sizes. In analogy to recent developments in the theory of graphs, posets and permutations we investigate some general aspects of the topology, such as a…
Maxmin trees are labeled trees with the property that each vertex is either a local maximum or a local minimum. Such trees were originally introduced by Postnikov, who gave a formula to count them and different combinatorial interpretations…
We reduce the calculation of the simplest Hodge integrals to some sums over decorated trees. Since Hodge integrals are already calculated, this gives a proof of a rather interesting combinatorial theorem and a new representation of…
Let $n$ be a prime power, $r$ be a prime with $r\mid n-1$, and $\varepsilon\in (0,1/2)$. Using the theory of multiplicative character sums and superelliptic curves, we construct new codes over $\mathbb F_r$ having length $n$, relative…
A quaternionic representation of the genetic code, previously reported by the authors, is updated in order to incorporate chirality of nucleotide bases and amino acids. The original representation assigns to each nucleotide base a prime…
We present a new universal source code for distributions of unlabeled binary and ordinal trees that achieves optimal compression to within lower order terms for all tree sources covered by existing universal codes. At the same time, it…
We use recurrence equations (alias difference equations) to enumerate the number of formula-representations of positive integers using only addition and multiplication, and using addition, multiplication, and exponentiation, where all the…
In this paper we investigate how a typical, large-dimensional representation looks for a complex Lie algebra. In particular, we study the family $\mathfrak{sl}_{r+1}(\mathbb{C})$ of Lie algebras for $r \geq 2$ and derive asymptotic…
By extending the breadth first search algorithm to any d-type critical or subcritical irreducible branching forest, we show that such forests may be encoded through d independent, integer valued, d-dimensional random walks. An application…
Tanglegrams are a special class of graphs appearing in applications concerning cospeciation and coevolution in biology and computer science. They are formed by identifying the leaves of two rooted binary trees. We give an explicit formula…
In light of the grammar given by Ji for the $(\alpha,\beta)$-Eulerian polynomials introduced by Carlitz and Scoville, we provide a labeling scheme for increasing binary trees. In this setting, we obtain a combinatorial interpretation of the…