Related papers: Combinatorics of Palindromes
We introduce new combinatorial objects, the interval- posets, that encode intervals of the Tamari lattice. We then find a combinatorial interpretation of the bilinear operator that appears in the functional equation of Tamari intervals…
Any graph which is not vertex transitive has a proper induced subgraph which is unique due to its structure or the way of its connection to the rest of the graph. We have called such subgraph as an anchor. Using an anchor which, in fact, is…
In this work we study the interleaving distance between merge trees from a combinatorial point of view. We use a particular type of matching between trees to obtain a novel formulation of the distance. With such formulation, we tackle the…
This paper considers a hyperplane arrangement constructed with a subset of a set of all simple paths in a graph. A connection of the constructed arrangement to the maximum matching problem is established. Moreover, the problem of finding…
The ''trace reconstruction'' problem asks, given an unknown binary string $x$ and a channel that repeatedly returns ''traces'' of $x$ with each bit randomly deleted with some probability $p$, how many traces are needed to recover $x$? There…
Labeled infinite trees provide combinatorial interpretations for many integer sequences generated by nested recurrence relations. Typically, such sequences are monotone increasing. Several of these sequences also have straightforward…
Pedigrees, or family trees, are graphs of family relationships that are used to study inheritance. A fundamental problem in computational biology is to find, for a pedigree with $n$ individuals genotyped at every site, a set of…
It is known that any chordal graph on $n$ vertices can be represented as the intersection of $n$ subtrees in a tree on $n$ nodes. This fact is recently used in [2] to generate random chordal graphs on $n$ vertices by generating $n$ subtrees…
A recurring theme in the least squares approach to phylogenetics has been the discovery of elegant combinatorial formulas for the least squares estimates of edge lengths. These formulas have proved useful for the development of efficient…
We build on recent work of Yeats, Courtiel, and others involving connected chord diagrams. We first derive from a Hopf-algebraic foundation a class of tree-like functional equations and prove that they are solved by weighted generating…
The reduction of the fragment assembly problem to (variations of) the classical Eulerian trail problem [Pevzner et al., PNAS 2001] has led to remarkable progress in genome assembly. This reduction employs the notion of de Bruijn graph…
Motivation: Word-based or `alignment-free' methods for phylogeny reconstruction are much faster than traditional approaches, but they are generally less accurate. Most of these methods calculate pairwise distances for a set of input…
We consider the problem of approximately reconstructing a partially-observed, approximately low-rank matrix. This problem has received much attention lately, mostly using the trace-norm as a surrogate to the rank. Here we study low-rank…
We give a novel combinatorial interpretation to the perturbative series solutions for a class of Dyson-Schwinger equations. We show how binary tubings of rooted trees with labels from an alphabet on the tubes, and where the labels satisfy…
The edge-reconstruction number of graph $G$, denoted $ern(G)$,is the size of the smallest multiset of edge-deleted, unlabeled subgraphs of $G$, from which the structure of $G$ can be uniquely determined. That there was some connection…
Spanners are fundamental graph structures that sparsify graphs at the cost of small stretch. In particular, in recent years, many sequential algorithms constructing additive all-pairs spanners were designed, providing very sparse…
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…
In [1], we introduced a family of combinatorial designs, which we call "alphabet reduction pairs of arrays", ARPAs for short. These designs depend on three integer parameters $q, p \leq q, k\leq p$: $q$ is the size of the symbol set $\{0, 1…
Secure codes are widely-studied combinatorial structures which were introduced for traitor tracing in broadcast encryption. To determine the maximum size of such structures is the main research objective. In this paper, we investigate the…
We show that the number of all maximal $\alpha$-gapped repeats and palindromes of a word of length $n$ is at most $3(\pi^2/6 + 5/2) \alpha n$ and $7 (\pi^2 / 6 + 1/2) \alpha n - 5 n - 1$, respectively.