Related papers: Combinatorics of Palindromes
Palindromes are popular and important objects in textual data processing, bioinformatics, and combinatorics on words. Let $S = XaY$ be a string where $X$ and $Y$ are of the same length, and $a$ is either a single character or the empty…
Squier introduced a homotopical method in order to describe all the relations amongst rewriting reductions of a confluent and terminating string rewriting system. From a string rewriting system he constructed a $2$-dimensional combinatorial…
Motivated by polymer-based data-storage platforms that use chains of binary synthetic polymers as the recording media and read the content via tandem mass spectrometers, we propose a new family of codes that allows for unique string…
In this paper, we study the combinatorial set of RNA secondary structures of length $n$ with $m$ base-pairs. For a compact representation, we encode an RNA secondary structure by the corresponding Motzkin word. For this combinatorial set,…
We describe a combinatorial approach for investigating properties of rational numbers. The overall approach rests on structural bijections between rational numbers and familiar combinatorial objects, namely rooted trees. We emphasize that…
Motivated by polymer-based data-storage platforms that use chains of binary synthetic polymers as the recording media and read the content via tandem mass spectrometers, we propose a new family of codes that allows for both unique string…
We study the problem of learning a node-labeled tree given independent traces from an appropriately defined deletion channel. This problem, tree trace reconstruction, generalizes string trace reconstruction, which corresponds to the tree…
We present a method which displays all palindromes of a given length from De Bruijn words of a certain order, and also a recursive one which constructs all palindromes of length $n+1$ from the set of palindromes of length $n$. We show that…
We suggest a new non-recursive algorithm for constructing a binary search tree given an array of numbers. The algorithm has $O(N)$ time and $O(1)$ memory complexity if the given array of $N$ numbers is sorted. The resulting tree is of…
In this article, we construct explicit examples of pairs of non-isomorphic trees with the same restricted $U$-polynomial for every $k$; by this we mean that the polynomials agree on terms with degree at most $k+1$. The main tool for this…
We consider the phylogenetic tree reconstruction problem with insertions and deletions (indels). Phylogenetic algorithms proceed under a model where sequences evolve down the model tree, and given sequences at the leaves, the problem is to…
Tree trace reconstruction aims to learn the binary node labels of a tree, given independent samples of the tree passed through an appropriately defined deletion channel. In recent work, Davies, R\'acz, and Rashtchian used combinatorial…
This paper introduces a new combinatorial framework for modeling the growth of binary trees through a discrete evolution process that incorporates a growing rule and an extinction rule. Building upon the theory of increasingly labeled…
A composition of a nonnegative integer (n) is a sequence of positive integers whose sum is (n). A composition is palindromic if it is unchanged when its terms are read in reverse order. We provide a generating function for the number of…
The problem called "String reconstruction from substrings" is a mathematical model of sequencing by hybridization that plays an important role in DNA sequencing. In this problem, we are given a blackbox oracle holding an unknown string…
We consider the well-studied pattern counting problem: given a permutation $\pi \in \mathbb{S}_n$ and an integer $k > 1$, count the number of order-isomorphic occurrences of every pattern $\tau \in \mathbb{S}_k$ in $\pi$. Our first result…
The family of graphs that can be constructed from isolated vertices by disjoint union and graph join operations are called cographs. These graphs can be represented in a tree-like representation termed parse tree or cotree. In this paper,…
In this work, we derive upper bounds on the cardinality of tandem duplication and palindromic deletion correcting codes by deriving the generalized sphere packing bound for these error types. We first prove that an upper bound for tandem…
Binary jumbled pattern matching asks to preprocess a binary string $S$ in order to answer queries $(i,j)$ which ask for a substring of $S$ that is of length $i$ and has exactly $j$ 1-bits. This problem naturally generalizes to…
The combinatorics of RNA plays a central role in biology. Mathematical biologists have several commonly-used models for RNA: words in a fixed alphabet (representing the primary sequence of nucleotides) and plane trees (representing the…